The 49ers has also re-signed safety Bubba Ventrone to a one-year deal.
Kilgore had season-ending surgery on Tuesday for his fractured left lower leg. Cook left the 49ers' game against the Denver Broncos on Sunday night with a hamstring injury. Matt Barrows of the Sacramento Bee reports that, according to a source, Cook suffered a torn hamstring.
The moves leave one roster spot open on the team. Matt Maiocco of CSN Bay Area points out that there is still a possibility that linebacker Aldon Smith's nine-game suspension may be reduced. Although, nothing has been officially announced by the league.
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